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  1. Article ; Online: An evolution of Nanopore next-generation sequencing technology: implications for medical microbiology and public health.

    Mostafa, Heba H

    Journal of clinical microbiology

    2024  , Page(s) e0024624

    Abstract: Next-generation sequencing has evolved as a powerful tool, with applications that extend from diagnosis to public health surveillance and outbreak investigations. Short-read sequencing, using primarily Illumina chemistry, has been the prevailing approach. ...

    Abstract Next-generation sequencing has evolved as a powerful tool, with applications that extend from diagnosis to public health surveillance and outbreak investigations. Short-read sequencing, using primarily Illumina chemistry, has been the prevailing approach. Single-molecule sensing and long-read sequencing using Oxford Nanopore Technologies (ONT) has witnessed a breakthrough in the evolution of the technology, performance, and applications in the past few years. In this issue of the
    Language English
    Publishing date 2024-04-02
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/jcm.00246-24
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  2. Article ; Online: Is It Possible to Test for Viral Infectiousness?: The Use Case of (SARS-CoV-2).

    Mostafa, Heba H

    Clinics in laboratory medicine

    2023  Volume 44, Issue 1, Page(s) 85–93

    Abstract: Identifying and managing individuals with active or chronic disease, implementing appropriate infection control measures, and mitigating the spread of the COVID-19 pandemic highlighted the need for tests of infectiousness. The gold standard for assessing ...

    Abstract Identifying and managing individuals with active or chronic disease, implementing appropriate infection control measures, and mitigating the spread of the COVID-19 pandemic highlighted the need for tests of infectiousness. The gold standard for assessing infectiousness has been the recovery of infectious virus in cell culture. Using cycle threshold values, antigen testing, and SARS-CoV-2, replication intermediate strands were used to assess infectiousness, with many limitations. Infectiousness can be influenced by host factors (eg, preexisting immune responses) and virus factors (eg, evolution).
    MeSH term(s) Humans ; SARS-CoV-2 ; COVID-19/diagnosis ; Pandemics ; Virus Diseases ; Infection Control
    Language English
    Publishing date 2023-11-13
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 604580-7
    ISSN 1557-9832 ; 0272-2712
    ISSN (online) 1557-9832
    ISSN 0272-2712
    DOI 10.1016/j.cll.2023.10.008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Next-generation sequencing for cytomegalovirus genotypic antiviral resistance testing.

    Mostafa, Heba H

    Journal of clinical microbiology

    2023  Volume 61, Issue 12, Page(s) e0130223

    Abstract: Sanger-based sequencing has long served as the gold standard for detecting cytomegalovirus (CMV) resistance mutations. However, next-generation sequencing (NGS) offers a highly multiplexed and sensitive approach. Clinical implementation of NGS-antiviral ... ...

    Abstract Sanger-based sequencing has long served as the gold standard for detecting cytomegalovirus (CMV) resistance mutations. However, next-generation sequencing (NGS) offers a highly multiplexed and sensitive approach. Clinical implementation of NGS-antiviral resistance testing requires thorough validation. In this issue of the Journal of Clinical Microbiology, M. A. Mallory, W. C. Hymas, K. E. Simmon, M. T. Pyne, et al. (J Clin Microbiol 61:e00829-23, 2023, https://doi.org/10.1128/jcm.00829-23) detail a validation of a targeted NGS-based assay for multiple genomic regions that confer resistance to CMV antivirals and share their bioinformatics analysis and reporting pipeline. This validation can serve as guidance for laboratories wishing to develop similar methodologies.
    MeSH term(s) Humans ; Cytomegalovirus/genetics ; High-Throughput Nucleotide Sequencing/methods ; Drug Resistance, Viral/genetics ; Cytomegalovirus Infections/diagnosis ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Mutation
    Chemical Substances Antiviral Agents
    Language English
    Publishing date 2023-11-22
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/jcm.01302-23
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  4. Article ; Online: Importance of internal controls to monitor adequate specimen collection: The case of orthopoxvirus real-time PCR.

    Mostafa, Heba H

    Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

    2022  Volume 156, Page(s) 105294

    MeSH term(s) DNA Primers ; Humans ; Orthopoxvirus/genetics ; Poxviridae Infections/diagnosis ; Real-Time Polymerase Chain Reaction ; Specimen Handling
    Chemical Substances DNA Primers
    Language English
    Publishing date 2022-09-14
    Publishing country Netherlands
    Document type Letter
    ZDB-ID 1446080-4
    ISSN 1873-5967 ; 1386-6532
    ISSN (online) 1873-5967
    ISSN 1386-6532
    DOI 10.1016/j.jcv.2022.105294
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    Zs.A 3790: Show issues Location:
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  5. Article ; Online: Recent Advances in

    H Baky, Mostafa / Fahmy, Heba / Farag, Mohamed A

    ACS omega

    2022  Volume 7, Issue 30, Page(s) 25948–25957

    Abstract: ... Garcinia ... ...

    Abstract Garcinia cambogia
    Language English
    Publishing date 2022-07-19
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.2c02838
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  6. Article ; Online: Validation and implementation of an orthopoxvirus qualitative real-time PCR for the diagnosis of monkeypox in the clinical laboratory.

    Uhteg, Katharine / Mostafa, Heba H

    Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

    2022  Volume 158, Page(s) 105327

    Abstract: Background: The globally concerning outbreak of monkeypox virus (MPXV) in non-endemic countries in 2022 warranted an increased capacity of diagnostic clinical testing. In this study, we detail the Johns Hopkins analytical validation of a qualitative ... ...

    Abstract Background: The globally concerning outbreak of monkeypox virus (MPXV) in non-endemic countries in 2022 warranted an increased capacity of diagnostic clinical testing. In this study, we detail the Johns Hopkins analytical validation of a qualitative orthopoxvirus real-time PCR and characterize its analytical performance for MPXV testing. We also describe our first month of MPXV clinical laboratory diagnosis, including assay utilization and positivity.
    Methods: The analytical performance of a previously characterized orthopoxvirus assay that targets the DNA polymerase gene of non-variola orthopoxviruses was determined. In silico inclusivity analysis was performed for the primer and probe sequences. The limit of detection, reproducibility, agreement, and specificity were evaluated as well as target stability at room temperature. Clinical chart reviews were performed for patients who received testing within the first month of offering the assay for diagnosis.
    Results: Alignment of the primer and probe binding regions of 151 sequenced genomes of MPXV from 2022 showed Sequence homology of 100%. The assay was able to detect MPXV at a concentration of at least 100 copies/mL and showed no cross reactivity with other organisms tested. Targets were stable for at least one week at room temperature. During the first month of implementation, a total of 33 patients were tested, 11 of whom were positive and presented mainly with rash in the genital region.
    Conclusions: Increased availability of MPXV testing is essential with the progressive increase in the number of cases. The non-variola orthopoxvirus assay is a sensitive and reproducible method for diagnosing monkeypox during the current surge in cases.
    MeSH term(s) Humans ; Mpox (monkeypox)/diagnosis ; Orthopoxvirus/genetics ; Real-Time Polymerase Chain Reaction ; Laboratories, Clinical ; Reproducibility of Results ; DNA, Viral/genetics ; Monkeypox virus/genetics
    Chemical Substances DNA, Viral
    Language English
    Publishing date 2022-11-11
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1446080-4
    ISSN 1873-5967 ; 1386-6532
    ISSN (online) 1873-5967
    ISSN 1386-6532
    DOI 10.1016/j.jcv.2022.105327
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Recent Advances in Garcinia cambogia Nutraceuticals in Relation to Its Hydroxy Citric Acid Level. A Comprehensive Review of Its Bioactive Production, Formulation, and Analysis with Future Perspectives

    Mostafa H. Baky / Heba Fahmy / Mohamed A. Farag

    ACS Omega, Vol 7, Iss 30, Pp 25948-

    2022  Volume 25957

    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2022-07-01T00:00:00Z
    Publisher American Chemical Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Increased circulation of human adenovirus in 2023: an investigation of the circulating genotypes, upper respiratory viral loads, and hospital admissions in a large academic medical center.

    Abdullah, Omar / Fall, Amary / Klein, Eili / Mostafa, Heba H

    Journal of clinical microbiology

    2023  Volume 62, Issue 1, Page(s) e0123723

    Abstract: Importance: The circulation of human adenoviruses (HAdV) increased in 2023. In this manuscript, we show that HAdV-B3 was predominant in 2023 in a cohort characterized by the Johns Hopkins Hospital System. We also show that HAdV-B3 was associated with an ...

    Abstract Importance: The circulation of human adenoviruses (HAdV) increased in 2023. In this manuscript, we show that HAdV-B3 was predominant in 2023 in a cohort characterized by the Johns Hopkins Hospital System. We also show that HAdV-B3 was associated with an increase in viral loads in respiratory samples and provide a correlation with the clinical presentations and outcomes.
    MeSH term(s) Humans ; Infant ; Adenoviruses, Human/genetics ; Adenovirus Infections, Human/diagnosis ; Adenovirus Infections, Human/epidemiology ; Viral Load ; Polymerase Chain Reaction ; Respiratory Tract Infections/diagnosis ; Respiratory Tract Infections/epidemiology ; Genotype ; Hospitals ; Academic Medical Centers ; Phylogeny
    Language English
    Publishing date 2023-12-19
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/jcm.01237-23
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  9. Article ; Online: Clinical performance evaluation of the Aptima viral assays for the quantitation of HIV-1, HCV, and HBV in plasma samples.

    Lewis, Shawna / Morehead, Elizabeth / Cheung, Helen / Mostafa, Heba H

    Diagnostic microbiology and infectious disease

    2023  Volume 106, Issue 3, Page(s) 115951

    Abstract: The clinical performance of the Aptima® HIV-1 Quant Dx, Aptima HCV Quant Dx, and Aptima HBV Quant Dx were evaluated and compared to the Roche cobas HIV-1, HCV, and HBV assays performed on the Roche cobas 6800 system. The Aptima Quant assays exhibited an ... ...

    Abstract The clinical performance of the Aptima® HIV-1 Quant Dx, Aptima HCV Quant Dx, and Aptima HBV Quant Dx were evaluated and compared to the Roche cobas HIV-1, HCV, and HBV assays performed on the Roche cobas 6800 system. The Aptima Quant assays exhibited an overall percent agreement of 99.4% for HBV, 98.3% for HCV, and 85.14% for HIV-1. The average log difference between the Aptima and Roche assays was below 0.2 IU (or copies)/mL and the quantitative correlation's (R-squared value (R
    MeSH term(s) Humans ; HIV-1/genetics ; Hepatitis B virus/genetics ; Viral Load ; Molecular Diagnostic Techniques ; Sensitivity and Specificity ; Hepatitis C/diagnosis ; RNA, Viral/genetics ; HIV Infections/diagnosis
    Chemical Substances RNA, Viral
    Language English
    Publishing date 2023-04-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 604920-5
    ISSN 1879-0070 ; 0732-8893
    ISSN (online) 1879-0070
    ISSN 0732-8893
    DOI 10.1016/j.diagmicrobio.2023.115951
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  10. Article ; Online: The use of thermal imaging for evaluation of peripheral tissue perfusion in surgical patients with septic shock.

    Hasanin, Ahmed / Fekry, Radwa / Mostafa, Maha / Kasem, Sahar / Eissa, Amany / Mohamed, Hassan / Raafat, Heba

    BMC anesthesiology

    2024  Volume 24, Issue 1, Page(s) 109

    Abstract: ... in (Celsius [°C]) were assessed at the time of admission, 6- and 12 h after admission. The canthal-toe and ... significant accuracy in predicting mortality at any timepoint. Only the toe temperature measurement at 12 h ...

    Abstract Background: In this study, we aimed to evaluate the ability of central-to-peripheral temperature gradients using thermal imaging to predict in-hospital mortality in surgical patients with septic shock.
    Methods: This prospective observational study included adult patients with septic shock admitted to the intensive care unit postoperatively. Serum lactate (in mmol/L), capillary refill time (CRT) (in seconds), toe (peripheral) and canthal (central) temperature by infrared thermography and the corresponding room temperature in (Celsius [°C]) were assessed at the time of admission, 6- and 12 h after admission. The canthal-toe and room-toe temperature gradients were calculated. According to their final outcomes, patients were divided into survivors and non-survivors. The ability of canthal-toe temperature gradient (primary outcome), room-toe temperature gradient, toe temperature, serum lactate and CRT, measured at the prespecified timepoints to predict in-hospital mortality was analyzed using the area under receiver operating characteristic curve (AUC).
    Results: Fifty-six patients were included and were available for the final analysis and 41/56 (73%) patients died. The canthal-toe and room-toe temperature gradients did not show significant accuracy in predicting mortality at any timepoint. Only the toe temperature measurement at 12 h showed good ability in predicting in-hospital mortality with AUC (95% confidence interval) of 0.72 (0.58-0.84) and a negative predictive value of 70% at toe temperature of ≤ 25.5 °C. Both serum lactate and CRT showed good ability to predict in-hospital mortality at all timepoints with high positive predictive values (> 90%) at cut-off value of > 2.5-4.3 mmol/L for the serum lactate and > 3-4.2 s for the CRT.
    Conclusion: In post-operative emergency surgical patients with septic shock, high serum lactate and CRT can accurately predict in-hospital mortality and were superior to thermal imaging, especially in the positive predictive values. Toe temperature > 25.5 °C, measured using infrared thermal imaging can exclude in-hospital mortality with a negative predictive value of 70%.
    MeSH term(s) Adult ; Humans ; Shock, Septic ; Prognosis ; ROC Curve ; Lactates ; Perfusion
    Chemical Substances Lactates
    Language English
    Publishing date 2024-03-21
    Publishing country England
    Document type Observational Study ; Journal Article
    ZDB-ID 2091252-3
    ISSN 1471-2253 ; 1471-2253
    ISSN (online) 1471-2253
    ISSN 1471-2253
    DOI 10.1186/s12871-024-02486-w
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